Liver Transcriptome Analysis of the Black Porgy (<i>Acanthopagrus schlegelii</i>) under Acute Low-Temperature Stress
High nutritional value and the development of efficient biotechnological methods of controlled production have made black porgy (<i>Acanthopagrus schlegelii</i>) an economically important fish in Chinese aquaculture in recent years. However, aquaculture production of the species faces mu...
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MDPI AG
2023-03-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/13/3/721 |
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| author | Yue Wang Ziqiang Chen Mingliang Wei Zhijie Lin Mingjun Shen Fei Zhu Chaofeng Jia Qian Meng Dafeng Xu Shuran Du Yanli Liu Shuyin Chen Caojin Zhang Zhiyong Zhang Zhiwei Zhang |
| author_facet | Yue Wang Ziqiang Chen Mingliang Wei Zhijie Lin Mingjun Shen Fei Zhu Chaofeng Jia Qian Meng Dafeng Xu Shuran Du Yanli Liu Shuyin Chen Caojin Zhang Zhiyong Zhang Zhiwei Zhang |
| author_sort | Yue Wang |
| collection | DOAJ |
| description | High nutritional value and the development of efficient biotechnological methods of controlled production have made black porgy (<i>Acanthopagrus schlegelii</i>) an economically important fish in Chinese aquaculture in recent years. However, aquaculture production of the species faces multiple issues associated with reduced growth rate, low reproduction ability, and high mortality during production, which are associated with the species’ limited tolerance to low temperatures. To date, comprehensive information on the genetic-based mechanisms of cold tolerance and adaptation to low temperature in the species are still unavailable. In this study, the HiSeq™2500 (Illumina) sequencing platform was used to analyze the transcriptomic profile of the liver tissue in the black porgy subjected to different extents of cold shock, including a control temperature group (AS, T = 15 °C), an intermediate temperature group (AL1, T = 10 °C), and an acute low-temperature stress group (AL2, T = 5 °C). For this purpose, three standardized cDNA libraries of AS, AL1, and AL2 were established. We obtained 43,258,908, 48,239,072, and 38,983,833 clean reads from the AS group, AL1 group, and AL2 group, respectively. After pairwise comparison, 70 differentially expressed genes (DEGs) were identified in the examined fish groups. Among them, 60 genes were found to be significantly differentially expressed after trend analysis. GO annotation and enrichment results showed that they were mainly enriched into three categories: biological processes (12 subcategories), molecular functions (7 subcategories), and cellular components (7 subcategories). KEGG analysis results indicated that all significantly differentially expressed genes were annotated to 102 signaling pathways, including biological rhythm, cholesterol metabolism, glycerolipid metabolism, animal autophagy, FoxO signaling pathway, steroid biosynthesis, and regulation of adipocyte lipolysis and apoptosis. Four of them, namely: G6PC, GPX1, GCK, and HSPE1 were randomly selected for further qRT-PCR verification of data reliability obtained by RNA-Seq technology. In this study, we found that environmental acute cold stress mainly affected the black porgy’s biological processes related to metabolism, apoptosis, and signal transduction. The data that we have reported provides baseline information for further studies concerning the genetic responses of the black porgy under cold stress conditions, the improvement of its aquaculture production, and other economically important matters regarding their limited tolerance to cold shock. |
| first_indexed | 2024-03-11T06:16:59Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-11T06:16:59Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
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| series | Life |
| spelling | doaj.art-29089d8c722341fbad34bd5223e855e12023-11-17T12:11:27ZengMDPI AGLife2075-17292023-03-0113372110.3390/life13030721Liver Transcriptome Analysis of the Black Porgy (<i>Acanthopagrus schlegelii</i>) under Acute Low-Temperature StressYue Wang0Ziqiang Chen1Mingliang Wei2Zhijie Lin3Mingjun Shen4Fei Zhu5Chaofeng Jia6Qian Meng7Dafeng Xu8Shuran Du9Yanli Liu10Shuyin Chen11Caojin Zhang12Zhiyong Zhang13Zhiwei Zhang14National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaJiangsu Marine Fishery Research Institute, Nantong 226007, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaHigh nutritional value and the development of efficient biotechnological methods of controlled production have made black porgy (<i>Acanthopagrus schlegelii</i>) an economically important fish in Chinese aquaculture in recent years. However, aquaculture production of the species faces multiple issues associated with reduced growth rate, low reproduction ability, and high mortality during production, which are associated with the species’ limited tolerance to low temperatures. To date, comprehensive information on the genetic-based mechanisms of cold tolerance and adaptation to low temperature in the species are still unavailable. In this study, the HiSeq™2500 (Illumina) sequencing platform was used to analyze the transcriptomic profile of the liver tissue in the black porgy subjected to different extents of cold shock, including a control temperature group (AS, T = 15 °C), an intermediate temperature group (AL1, T = 10 °C), and an acute low-temperature stress group (AL2, T = 5 °C). For this purpose, three standardized cDNA libraries of AS, AL1, and AL2 were established. We obtained 43,258,908, 48,239,072, and 38,983,833 clean reads from the AS group, AL1 group, and AL2 group, respectively. After pairwise comparison, 70 differentially expressed genes (DEGs) were identified in the examined fish groups. Among them, 60 genes were found to be significantly differentially expressed after trend analysis. GO annotation and enrichment results showed that they were mainly enriched into three categories: biological processes (12 subcategories), molecular functions (7 subcategories), and cellular components (7 subcategories). KEGG analysis results indicated that all significantly differentially expressed genes were annotated to 102 signaling pathways, including biological rhythm, cholesterol metabolism, glycerolipid metabolism, animal autophagy, FoxO signaling pathway, steroid biosynthesis, and regulation of adipocyte lipolysis and apoptosis. Four of them, namely: G6PC, GPX1, GCK, and HSPE1 were randomly selected for further qRT-PCR verification of data reliability obtained by RNA-Seq technology. In this study, we found that environmental acute cold stress mainly affected the black porgy’s biological processes related to metabolism, apoptosis, and signal transduction. The data that we have reported provides baseline information for further studies concerning the genetic responses of the black porgy under cold stress conditions, the improvement of its aquaculture production, and other economically important matters regarding their limited tolerance to cold shock.https://www.mdpi.com/2075-1729/13/3/721transcriptomeblack porgy and low-temperature stress |
| spellingShingle | Yue Wang Ziqiang Chen Mingliang Wei Zhijie Lin Mingjun Shen Fei Zhu Chaofeng Jia Qian Meng Dafeng Xu Shuran Du Yanli Liu Shuyin Chen Caojin Zhang Zhiyong Zhang Zhiwei Zhang Liver Transcriptome Analysis of the Black Porgy (<i>Acanthopagrus schlegelii</i>) under Acute Low-Temperature Stress Life transcriptome black porgy and low-temperature stress |
| title | Liver Transcriptome Analysis of the Black Porgy (<i>Acanthopagrus schlegelii</i>) under Acute Low-Temperature Stress |
| title_full | Liver Transcriptome Analysis of the Black Porgy (<i>Acanthopagrus schlegelii</i>) under Acute Low-Temperature Stress |
| title_fullStr | Liver Transcriptome Analysis of the Black Porgy (<i>Acanthopagrus schlegelii</i>) under Acute Low-Temperature Stress |
| title_full_unstemmed | Liver Transcriptome Analysis of the Black Porgy (<i>Acanthopagrus schlegelii</i>) under Acute Low-Temperature Stress |
| title_short | Liver Transcriptome Analysis of the Black Porgy (<i>Acanthopagrus schlegelii</i>) under Acute Low-Temperature Stress |
| title_sort | liver transcriptome analysis of the black porgy i acanthopagrus schlegelii i under acute low temperature stress |
| topic | transcriptome black porgy and low-temperature stress |
| url | https://www.mdpi.com/2075-1729/13/3/721 |
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